Category Archives: Plant Root Soil microbiome

January 8, 2018

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Today’s Microbiome Digest has many interesting articles. Read how microscope-based artificial intelligence could alleviate shortage of clinical microbiologists, the article by K. P. Smith. N. A. Kamennaya reports on “Pomacytosis”, a semi-extracellular phagocytosis of cyanobacteria, while M. F. Dias investigated the effect of different drinking waters on mouse gut microbiota.

Events

One-day Symposium (12 Jan 2018): Microbial symbiosis in the marine environment – live streamming

Jobs

Postdoctoral positions in evolutionary genomics, UT Austin

General microbiome

Dietary trehalose enhances virulence of epidemic Clostridium difficile – J. Collins – Nature

Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla – Frederick M. Cohan – Microbiology Spectrum

How much do rRNA gene surveys underestimate extant bacterial diversity? – Luis M. Rodriguez-R – Applied and Environmental Microbiology

Vibrio cholerae genomic diversity within and between patients –  Inès Levade – Microbial Genomics

Automated Interpretation of Blood Culture Gram Stains using a Deep Convolutional Neural Network – Kenneth P. Smith – Applied and Environmental Microbiology

Regulated ploidy of Bacillus subtilis and three new isolates of Bacillus and Paenibacillus – Benjamin Böttinger – FEMS Microbiology Letters

Human respiratory microbiome

Heavy metal exposure and nasal Staphylococcus aureus colonization: analysis of the National Health and Nutrition Examination Survey (NHANES) – Shoshannah Eggers – Environmental Health

Oral microbiome

Microbial Analysis of Endodontic Infections in Root-filled Teeth with Apical Periodontitis before and after Irrigation Using Pyrosequencing – Homan Zandi – Journal of Endodontics

Human vaginal microbiome

Long-term Lactobacillus rhamnosus BMX 54 application to restore a balanced vaginal ecosystem: a promising solution against HPV-infection – Ettore Palma – BMC Infectious Diseases

Lactobacillus-deficient vaginal microbiota dominate post-partum women in rural Malawi – Ronan Doyle – Applied and Environmental Microbiology

Human nearly-sterile sites

Microbiota and the liver – Ting-Chin David Shen – Liver Transplatation

Human gut microbiome

Comparison of DNA extraction methods for human gut microbial community profiling – Mi Young Lim – Systematic and Applied Microbiology

Changes in Gut Microbiota–Related Metabolites and Long-term Successful Weight Loss in Response to Weight-Loss Diets: The POUNDS Lost Trial – Yoriko Heianza – Diabetes Care

Adaptation of human gut microbiota to bariatric surgeries in morbidly obese patients: A systematic review – Hanieh-Sadat Ejtahed – Microbial Pathogenesis

The germ-organ theory of non-communicable diseases – Mariana X. Byndloss – Nature Reviews Microbiology

Evolution of a dominant natural isolate of Escherichia coli in the human gut over a year suggests a neutral evolution with reduced effective population size – Mohamed Ghalayini – Applied and Environmental Microbiology

Animal experiments

Changes in mouse gut bacterial community in response to different types of drinking water – Marcela F. Dias – Water Research

Plant, root, and soil microbiome

Microbial Communities of High-Elevation Fumaroles, Penitentes, and Dry Tephra “Soils” of the Puna de Atacama Volcanic Zone – Adam J. Solon – Microbial Ecology

Shifts in soil bacterial and archaeal communities during freeze-thaw cycles in a seasonal frozen marsh, Northeast China – Jiusheng Ren – Science of The Total Environment

The ‘Neglected’ Soil Virome – Potential Role and Impact – Akbar Adjie Pratama – Trends in Microbiology

Water and extremophile microbiome 

Study of marine bacteria inactivation by photochemical processes: disinfection kinetics and growth modeling after treatment – Javier Moreno-Andrés – Environmental Science and Pollution Research

Metabolic capability and in situ activity of microorganisms in an oil reservoir – Yi-Fan Liu – Microbiome

Phylogenetic distribution of roseobacticides in the Roseobacter group and their effect on microalgae – Eva C Sonnenschein – BioRxiv

“Pomacytosis”—Semi-extracellular phagocytosis of cyanobacteria by the smallest marine algae – Nina A. Kamennaya – PLOS Biology

The Green Berry Consortia of the Sippewissett Salt Marsh: Millimeter-Sized Aggregates of Diazotrophic Unicellular Cyanobacteria – Elizabeth G. Wilbanks – Frontiers in Microbiology

Dynamic changes in carbonate chemistry in the microenvironment around single marine phytoplankton cells – Abdul Chrachri – Nature Communications

Homogenization of lake cyanobacterial communities over a century of climate change and eutrophication – Marie-Eve Monchamp – Nature Ecology & Evolution

Bacterial Recycling of Archaeal Biomass as a New Strategy for Extreme Life in the Dead Sea Deep Sediment – Camille Thomas – EarthArXiv Preprints

Food microbiology

Seasonal variances in bacterial microbiota and volatile organic compounds in raw milk – Beata Nalepa – International Journal of Food Microbiology

Phages and viruses

Is weak CD4+ gain in the course of suppressive combination antiretroviral therapy for HIV infection a current clinical challenge? A case report and brief review of the literature – Camilla Tincati – BMC Infectious Diseases

Techniques

NanoAmpli-Seq: A workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform – Szymon T Calus – bioRxiv

Microbes in the news

Scientists engineer sound-reflecting bacteria

Experts: ‘Raw Water’ Offers Unfiltered Risk

 

January 6, 2018

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Today’s digest features a lot of great “gut microbiome papers”, with a focus on precision medicine.

Events and jobs
Scientist, Computational Biology – Flagship Pioneering, VL45  Company LocationCambridge, Massachusetts

Human gut microbiome
** Microbiota Accessible Carbohydrates Facilitate Clearance of Clostridium difficile – Andrew J Hryckowian – bioRxiv **

** Precision medicine using microbiota – Christian Jobin – Science
Highlights three articles, including:
* The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients – Vyara Matson – Science
* Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors – Bertrand Routy – Science
* Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients – V. Gopalakrishnan – Science **

Exploring Gut Microbiota Composition as an Indicator of Clinical Response to Dietary FODMAP Restriction in Patients with Irritable Bowel Syndrome – Jørgen Valeur – Digestive Diseases And Sciences

Mucus Microbiome of Anastomotic Tissue During Surgery Has Predictive Value for Colorectal Anastomotic Leakage – Jasper B van Praagh – Annals Of Surgery

Review: Local Acetaldehyde-An Essential Role in Alcohol-Related Upper Gastrointestinal Tract Carcinogenesis – Mikko T Nieminen – Cancers

Review: The Gut-Brain Axis and the Microbiome: Clues to Pathophysiology and Opportunities for Novel Management Strategies in Irritable Bowel Syndrome (IBS). – Eamonn M M Quigley – Journal Of Clinical Medicine

Animal experiments
** Precision editing of the gut microbiota ameliorates colitis – Wenhan Zhu – Nature **

Polystyrene microplastics induce microbiota dysbiosis and inflammation in the gut of adult zebrafish – Yuanxiang Jin – Environmental Pollution

Profiling the lymphoid-resident T cell pool reveals modulation by age and microbiota – Aurélie Durand – Nature Communications

Cultivable anaerobic and aerobic bacterial communities in the fermentation chambers of Holotrichia parallela (coleoptera: scarabaeidae) larvae – Zhen-Yu Zhang – Plos One

The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota – Henrik Krehenwinkel – Plos One

The evaluation of the quality of Feng Huang Oolong teas and their modulatory effect on intestinal microbiota of high-fat diet-induced obesity mice model – Yuhui Chen – International Journal Of Food Sciences And Nutrition

Animal microbiome
Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth – Duc Lu – Microbiome

Review: Recent insights into the tick microbiome gained through next-generation sequencing – Telleasha L Greay – Parasites & Vectors

Plant, root, and soil microbiome
Responses of soil bacterial community after seventh yearly applications of composted tannery sludge – Ana Roberta Lima Miranda – Geoderma

Assessment of Cu applications in two contrasting soils—effects on soil microbial activity and the fungal community structure – Katharina M. Keiblinger – Ecotoxicology

Microorganisms reveal what plants do not: wheat growth and rhizosphere microbial communities after Azospirillum brasilense inoculation and nitrogen fertilization under field conditions – Luciana P. Di Salvo – Plant and Soil

16S rRNA analysis of diversity of manure microbial community in dairy farm environment – Pramod Pandey – Plos One

Agricultural constraints on microbial resource use and niche breadth in drainage ditches – Ellard R Hunting – Peerj

Water and extremophile microbiome
Accessing chemical diversity from the uncultivated symbionts of small marine animals – Thomas E Smith – Nature Chemical Biology

Macroalgal-bacterial interactions: Role of dimethylsulfoniopropionate in microbial gardening by Ulva (Chlorophyta) – Ralf W. Kessler – Molecular Ecology

Bacterial Recycling of Archaeal Biomass as a New Strategy for Extreme Life in the Dead Sea Deep Sediment – Camille Thomas – EarthArXiv

Unravelling the identity, metabolic potential, and global biogeography of the atmospheric methane-oxidising Upland Soil Cluster α – Jennifer Pratscher – Environmental Microbiology

Book: Optimization and Applicability of Bioprocesses – Hemant J. Purohit and other editors
Articles of interest include:
* Microbial CO2 Fixation Bioprocesses and Desert as Future Carbon Sink – Leena Agarwal
* Biofilm Microenvironments: Modeling Approach – Saheli Ghosh
* Visualization of Microorganisms in Bioprocesses – Tsuyoshi Yamaguchi

Built environment
The effect of temperature on airborne filamentous fungi in the indoor and outdoor space of a hospital – Fariba Abbasi – Environmental Science and Pollution Research

Probiotics / prebiotics / antibiotics
Cross-feeding modulates antibiotic tolerance in bacterial communities – Elizabeth M Adamowicz – bioRxiv

Review: Immune-Mediated Mechanisms of Action of Probiotics and Synbiotics in Treating Pediatric Intestinal Diseases – Julio Plaza-Díaz – Nutrients

Review: How Sweet Are Our Gut Beneficial Bacteria? A Focus on Protein Glycosylation in Lactobacillus. – Dimitrios Latousakis – International Journal Of Molecular Sciences

Phages and viruses
Review: Interactions between Enteric Bacteria and Eukaryotic Viruses Impact the Outcome of Infection – Angela K Berger – Viruses

Bioinformatics
Techniques
News Feature: Can microbes keep time for forensic investigators? – Carolyn Beans – PNAS

Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise – Taha Soliman – Peerj

Microbes in the news
Caltech breakthrough: Bacteria engineered with ‘sonar’ can track, fight disease – Eric Rosenbaum – CNBC

Microbes on the market
Can’t sleep? It could be your microbiome, says this Cambridge startup – Max Stendahl  – Boston Business Journal

Rebiotix and CoreBiome Collaborate on Evaluating Microbiomes of Patients Treated with Microbiota Restoration Therapy™ – Markets Insider

Seres Therapeutics Reports SER-287 Phase 1b Microbiome Analyses that Provide Mechanistic Support for Clinical Efficacy in Ulcerative Colitis – PipelineReview.com

January 5, 2018

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Today’s digest has an interesting commentary on the oral-gut connection and a brilliant piece on microbial diversity. Lastly, a look at how grapevines influence belowground diversity and networks

General Microbiome

A role for the endometrial microbiome in dysfunctional menstrual bleeding. Pelzer ES. Antonie Van Leeuwenhoek.

Performance and microbial community variations of anaerobic digesters under increasing tetracycline concentrations. Xiong Y. Applied Microbiology and Biotechnology

In Nature, There Is Only Diversity. McLaren MR. MBio.

Gut Microbiome

Commentary: Oral-gut connection: one step closer to an integrated view of the gastrointestinal tract? Lira-Junior R. Mucosal Immunology

Bile acids at the cross-roads of gut microbiome-host cardiometabolic interactions. Ryan PM. Diabeticology and Metabolic Syndrome

REVIEW: Diet, Microbiota, and Metabolic Health: Trade-Off Between Saccharolytic and Proteolytic Fermentation. Korpela K. Annual of Food Science and Technology

Nasal and Lung Microbiome

REVIEW: Fungi in Bronchiectasis: A Concise Review. Máiz L. Internatioanal Journal of Molecular Sciences

Alterations in the mucosa-associated fungal microbiota in patients with ulcerative colitis. Qiu X. Oncotarget

The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis. Luna PN. Microbiome

Fecal Microbiome

Editorial Comment: Fecal microbiota transplantation as a possible treatment of irritable bowel syndrome. Juncadella AC. Annals of Translational Medicine

Plant, Soil, and Water Microbiome

Co-variation between Distribution of Microbial Communities and Biological Metabolization of Organics in Urban Sewer Systems. Jin P. Environmental Science and Technology.

Do invasive plants structure microbial communities to accelerate decomposition in intermountain grasslands? McTee MR. Ecology and Evolution

Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality. Marasco R. Microbiome

Biodiversity of the microbial mat of the Garga hot spring. Rozanov AS. BMC Evolutionary Biology

Animal Experiments and Microbiome

Microbiota Reconstitution Does Not Cause Bone Loss in Germ-Free Mice. Quach D. mSphere

Physiological Translocation of Lactic Acid Bacteria during Pregnancy Contributes to the Composition of the Milk Microbiota in Mice. de Andrés J. Nutrients

Extreme sensitivity to ultraviolet light in the fungal pathogen causing white-nose syndrome of bats. Palmer JM. Nature Communication

OCCURRENCE OF PASTEURELLACEAE BACTERIA IN THE ORAL CAVITY OF SELECTED MARSUPIAL SPECIES. Hansen MJ. Journal of Zoo and Wildlife Medicine

Marine Microbiome

Agelas Wasting Syndrome Alters Prokaryotic Symbiont Communities of the Caribbean Brown Tube Sponge, Agelas tubulata.Deignan LK. Microbial Ecology

Environmental drivers of heterogeneity in the trophic-functional structure of protozoan communities during an annual cycle in a coastal ecosystem. Xu G. Marine Pollution Bulletin

Antibiotic Resitance

Editorial: Empiric antibiotic use in allogeneic hematopoietic cell transplantation: should we avoid anaerobe coverage? Shono Y. Blood Advances

Characterization of genetic determinants involved in antibiotic resistance in Aeromonas spp. and fecal coliforms isolated from different aquatic environments. Carnelli A. Research in Microbiology

 

 

January 4, 2017

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Implication of dysbiosis in arthritis in rats, studying soil crust biology and chemistry using metabolomics, a news article on exercise and the microbiome.

Human gut microbiome

Comprehensive analysis of polyamine transport and biosynthesis in the dominant human gut bacteria: Potential presence of novel polyamine metabolism and transport genes – Yuta Sugiyama – The International Journal of Biochemistry & Cell Biology

Animal experiments

Effects of HLA-B27 on Gut Microbiota in Experimental Spondyloarthritis Implicate an Ecological Model of Dysbiosis – Tejpal Gill – Arthritis & Rheumatology

Plant, root, and soil microbiome

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics – Tami L Swenson – Nature Communications

Cooperative interactions between seed-borne bacterial and air-borne fungal pathogens on rice – Boknam Jung – Nature Communications

Synergistic action of rhizospheric fungi with Megathyrsus maximus root speeds up hydrocarbon degradation kinetics in oil polluted soil – Michael Dare Asemoloye – Chemosphere

Pre-print: Crop diversity increases disease suppressive capacity of soil microbiomes – Ariane L Peralta – bioRxiv

Microbes in the news

Exercise Alters Our Microbiome. Is That One Reason It’s So Good for Us? – Gretchen Reynolds – The New York Times

Bifidobacterium or fiber protect against deterioration of the inner colonic mucus layer – ScienceDaily

Scientists use sound to track tiny organisms in the body – Angela Chen – The Verge

Bacteria and Cancer: Another Connection – Derek Lowe – Science Translational Medicine

January 2, 2018

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Happy New Year from the Microbiome Digest team!

General microbiome

Pre-print: Understanding How Microbiomes Influence The Systems They Inhabit: moving from a correlative to a causal research framework – E K Hall – bioRxiv

Human vaginal microbiome

A retrospective pilot study to determine whether the reproductive tract microbiota differs between women with a history of infertility and fertile women – Bryan A Wee – Australian and New Zealand Journal of Obstetrics and Gynaecology

Human gut microbiome

Rates of Gut Microbiome Divergence in Mammals – Alex H Nishida – Molecular Ecology

Animal microbiome

Processes shaping gut microbiota diversity in allopatric populations of the endemic lizard Podarcis lilfordi from Menorcan islets (Balearic Islands) – Laura Baldo – FEMS Microbiology Ecology

Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing – Kathrin Engel – Microbial Ecology

Plant, root, and soil microbiome

Vertical variation of a black soil’s properties in response to freeze-thaw cycles and its links to shift of microbial community structure – Ziming Han – Science of the Total Environment

Biomass, activity and structure of rhizosphere soil microbial community under different metallophytes in a mining site – Wenhao Yang – Plant and Soil

Symbiotic nitrogen fixation by rhizobia — the roots of a success story – Catherine Masson-Boivin – Current Opinion in Plant Biology

Water and extremophile microbiome

Microbial community structure and function in sediments from e-waste contaminated rivers at Guiyu area of China – Jun Liu – Environmental Pollution

Pre-print: Micro-scale ecology regulates particulate organic matter turnover in model marine microbial communities – Tim N Enke – bioRxiv

Food microbiology

Autochthonous facility-specific microbiota dominates washed-rind Austrian hard cheese surfaces and its production environment – Narciso M Quijada – International Journal of Food Microbiology

Bioinformatics

CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision – Damayanthi Herath – BMC Bioinformatics

Techniques

Serial Dilution-Based Growth Curves and Growth Curve Synchronization for High-Resolution Time Series of Bacterial Biofilm Growth – Fernando Govantes – Host-Pathogen Interactions

Microbes in the news

Fiber Is Good for You. Now Scientists May Know Why. – Carl Zimmer – The New York Times

Fast, Cheap Testing for Tuberculosis? Soon It May Be Possible – Donald G McNeil – The New York Times

How probiotics can help ward off health complications in premature babies – CTV News

Science, career, and publishing

Pre-print: Disequilibrium in Gender Ratios among Authors who Contributed Equally – Nichole A Broderick – bioRxiv

December 31, 2017

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A rich Digest to end 2017! There are several reviews on human gut microbiome and lots of papers on plant , root and soil microbiome. The airway microbiome is trending today and scientists are starting to examine rigorously the effect of herbal medicine on the gut microbiota. Happy Reading and Happy New Year!

General microbiology

Bacterial pathogens were detected from human exhaled breath using a novel protocol – Yunhao Zheng et al. – Journal of Aerosol Science

Bacteria Facilitate Enteric Virus Co-infection of Mammalian Cells and Promote Genetic Recombination – Andrea K. Erickson et al. – Cell Host & Microbe

Human airway microbiome

Review: Airway microbial metagenomics – Katarzyna Pienkowska et al. – Microbes and Infection

Respiratory syncytial virus and rhinovirus bronchiolitis are associated with distinct metabolic pathways – Christopher J Stewart et al. – Journal of Infectious Diseases

Tech Note: A breath of information: the volatilome – M. Mansurova et al. – Current Genetics

Short-term particulate matter exposure influences nasal microbiota in a population of healthy subjects – Jacopo Mariani et al. – Environmental Research

Exposure to traffic-related air pollution and the composition of the gut microbiota in overweight and obese adolescents – Tanya L. Alderete et al. – Environmental Research

Human gut microbiome

Gut microbiome contributes to impairment of immunity in pulmonary tuberculosis patients by alteration of butyrate and propionate producers – Abhijit Maji et al. – Environmental Microbiology

Review: Targeting the gut barrier for the treatment of alcoholic liver disease – Zhanxiang Zhou and Wei Zhong – Liver Research

Review: Microbial Regulation of Glucose Metabolism and Insulin Resistance – Crommen S and Simon MC – Genes

Review: Gut microbiota in the pathogenesis of inflammatory bowel disease – Nishida A et al. – Clinical Journal of Gastroenterology

Review: Human Intestinal Microbiota: Interaction Between Parasites and the Host Immune Response – Oswaldo Partida-Rodríguez et al. – Archives of Medical Research

Review: Gut dysbiosis and irritable bowel syndrome: the potential role of probiotics – Nicola Principi et al. – Journal of Infection

Review: Gut Microbiota in Obesity and Metabolic Abnormalities: A Matter of Composition or Functionality? – Sofia Moran-Ramo et al. – Archives of Medical Research

In vitro: An in vitro study to assess the impact of tetracycline on the human intestinal microbiome – Ji Young Jung et al. – Anaerobe

Human gut-microbiome-brain axis

Review: Targeting gut microbiome: A novel and potential therapy for autism – Yongshou Yang et al. – Life Sciences

Metabolomics

Dark matter in host-microbiome metabolomics: Tackling the unknowns–A review – B.Y. Loulou Peisl et al. – Analytica Chimica Acta

Animal experiments

Mouse: Intestinal Ralstonia pickettii augments glucose intolerance in obesity – Shanthadevi D. Udayappan et al. – PLoS One

Pig: Structural Modulation of Gut Microbiota during Alleviation of Suckling Piglets Diarrhoea with Herbal Formula – Cui Liu et al. – Evidence-Based Complementary and Alternative Medicine

Rat: Effects of HLA-B27 on Gut Microbiota in Experimental Spondyloarthritis Implicate an Ecological Model of Dysbiosis – Gill T et al. – Arthritis and Rheumatology

Changes in mouse gut bacterial community in response to different types of drinking water – Marcela F. Dias et al. – Water Research

Mouse: Particle size determines the anti-inflammatory effect of wheat bran in a model of fructose over-consumption: Implication of the gut microbiota – Francesco Suriano & Audrey M. Neyrinck et al. – Journal of Functional Foods

Mouse: Mushroom polysaccharides from Ganoderma lucidum and Poria cocos reveal prebiotic functions – Imran Khan et al. – Journal of Functional Foods

Animal microbiome

Bacterial diversity of wild-caught Lutzomyia longipalpis (a vector of zoonotic visceral leishmaniasis in Brazil) under distinct physiological conditions by metagenomics analysis – Ana Clara Araújo Machado Pires et al. – Parasites & Vectors

Drosophila Perpetuates Nutritional Mutualism by Promoting the Fitness of Its Intestinal Symbiont Lactobacillus plantarum – Gilles Storelli et al. – Cell Metabolism

Analysis of the influence of living environment and age on vaginal fungal microbiome in giant pandas (Ailuropoda melanoleuca) by high throughput sequencing – Danyu Chen et al. – Microbial Pathogenesis

Plant, root and soil microbiome

Phosphate levels influence the utilisation of rice rhizodeposition carbon and the phosphate-solubilising microbial community in a paddy soil – Xi-En Long et al. – Soil Biology and Biochemistry

Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms – Aspen T. Reese et al. – Ecology and Evolution

Responses of bulk and rhizosphere soil microbial communities to thermoclimatic changes in a Mediterranean ecosystem – Javier Pascual et al. – Soil Biology and Biochemistry

Remediation of arsenic in mung bean (Vigna radiata) with growth enhancement by unique arsenic-resistant bacterium Acinetobacter lwoffii – Joyati Das and Priyabrata Sarkar – Science of the Total Environment
https://www.sciencedirect.com/science/article/pii/S0048969717335830

* Opinion: Why we need a National Living Soil Repository – Daniel K. Manter et al. – PNAS

Long-term effects of nitrogen fertilization on aggregation and localization of carbon, nitrogen and microbial activities in soil – Yidong Wang et al. – Science of the Total Environment

Vineyard microbiome variations during different fertilisation practices revealed by 16s rRNA gene sequencing – Loredana Canfora et al. – Applied Soil Ecology

* Co-occurrence patterns of soybean rhizosphere microbiome at a continental scale – Baogang Zhang et al. – Soil Biology and Biochemistry

Review: Symbiotic nitrogen fixation by rhizobia — the roots of a success story – Catherine Masson-Boivin and Joel L Sachs – Current Opinion in Plant Biology

Water and extremophile microbiome

PDF: From extreme environments to human pathogens: an evolutionary journey – Donato Giovannelli and Costantino Vetriani – Biochemical Society

Comparison of Iris pseudacorus wetland systems with unplanted systems on pollutant removal and microbial community under nanosilver exposure – Juan Huang et al. – Science of the Total Environment

Impacts of design configuration and plants on the functionality of the microbial community of mesocosm-scale constructed wetlands treating ibuprofen – Liang Zhang et al. – Water Research

Microbial community evolution in partial nitritation/anammox process: From sidestream to mainstream – Yandong Yang et al. – Bioresource Technology

Spatiotemporal changes in bacterial community and microbial activity in a full-scale drinking water treatment plant – Luanfeng Hou et al. – Science of the Total Environment

Built environment microbiome

Microbiological air contamination in university premises and the evaluation of drug resistance of staphylococci occurring in the form of a bioaerosol – Katarzyna Wolny-Koładka et al. – Indoor and Built Environment

Phages and viruses

Virome analysis of lily plants reveals a new potyvirus – Yongqiang Li et al. – Archives of Virology

Comparative Analysis of 37 Acinetobacter Bacteriophages – Dann Turner et al. – Viruses

Antiviral systems in vector mosquitoes – Tong Liu et al. – Developmental & Comparative Immunology

Microbes in the news

Launceston associate professors studying gut microbiome in elderly Tasmanians – Carly Dolan – Examiner

Biofilm made of mulberry silk to destroy dengue virus – TNN – Times of India

Rhode Island Health Department finds E. coli bacteria, issues boil water notice – PATRICIA RESENDE & TONY GUGLIOTT – NBC 10

Op-Ed: Survival tips in the age of drug-resistant bacteria – Kevin Kavanagh – Lexington Herald Leader

* One Big Family: This Beautiful Interactive Diagram Shows How Every Organism Is Related – Fiona McMillan – Forbes

Researchers propose different approach to beat antibiotic-resistant superbugs – News Medical

 

December 30, 2017

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Enjoy your daily dose of (mostly human gut) microbiome literature!

General microbiome

Q&A: Friends (but sometimes foes) within: the complex evolutionary ecology of symbioses between host and microbes – Nicole Gerardo, BMC Biology

The Dark Side of IFN-γ: Its Role in Promoting Cancer Immunoevasion – Marija Mojic, International Journal of Molecular Sciences

Two-stage pretreatment of excess sludge for electricity generation in microbial fuel cell – Yi Zhang, Environmental Technology

Human respiratory microbiome

Azithromycin versus placebo for the treatment of HIV-associated chronic lung disease in children and adolescents (BREATHE trial): study protocol for a randomised controlled trial – Carmen Gonzalez-Martinez, BMC Biology

Human skin microbiome

Characterization of the facial microbiome in twins discordant for rosacea – Asifa K. Zaidi, Experimental Dermatology

Human oral microbiome

Oral health in geroscience: animal models and the aging oral cavity – Jonathan Y. An, GeroScience

Extracellular matrix Influence in Streptococcus mutans gene expression in a cariogenic biofilm – Elkin Jahir Florez Salamanca, Molecular Oral Microbiology

Human gut microbiome

The Microbiome–Gut–Behavior Axis: Crosstalk Between the Gut Microbiome and Oligodendrocytes Modulates Behavioral Responses – Achilles Ntranos, Neurotherapeutics

Antibiotics Associated Disorders and Postbiotics Induced Rescue in Gut Health – Debarati Paul, Current Pharmaceutical Design

We are not alone in our body: insights into the involvement of microbiota in the etiopathogenesis and pharmacology of mental illness –  Claudia Pisanu, Current Drug Metabolism

Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003 – Francesca Bottacini, BMC Genomics

Microbiota dysbiosis in inflammatory bowel diseases: in silico investigation of the oxygen hypothesis – Michael A. Henson, BMC Systems Biology

Gut microbiota: Fibre restores healthy gut microbiota – Alan Morris, Nature Reviews Endocrinology

The human microbiome in evolution – Emily R. Davenport, BMC Biology

Clinical characteristics and long-term prognosis of elderly onset ulcerative colitis – Eun Mi Song, Gastroenterology and Hepatology

Environmental contributions to gastrointestinal and liver cancer in the Asia–Pacific region – Kwang-Pil Ko, Gastroenterology and Hepatology

Effect of oral tobacco use and smoking on outcomes of Crohn’s disease in India – Umang Arora, Gastroenterology and Hepatology

Irritable bowel syndrome in Asia: Pathogenesis, natural history, epidemiology, and management – Kok-Ann Gwee, Gastroenterology and Hepatology

Rifaximin has minor effects on bacterial composition, inflammation, and bacterial translocation in cirrhosis: A randomized trial – Nina Kimer, Gastroenterology and Hepatology

The role of the microbiome and the use of probiotics in gastrointestinal disorders in adults in the Asia-Pacific region – background and recommendations of a regional consensus meeting – Uday C Ghoshal, Gastroenterology and Hepatology

Animal experiments

Inclusion of Bacillus amyloliquefaciensstrain TOA5001 in the diet of broilers suppresses the symptoms of coccidiosis by modulating intestinal microbiota – Takamitsu Tsukahara, Animal Science Journal

Characterization of the cervical bacterial community in dairy cows with metritis and during different physiological phases – Yu Wang, Theriogenology

Replacement of alfalfa hay (Medicago sativa L.) with subabul (Leucaena leucocephala) leaf meal in diets of Najdi goats: effect on digestion activity of rumen microorganisms – Tahereh Mohammadabadi, Tropical Animal Health and Production

Animal microbiome

Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing – Kathrin Engel, Microbial Ecology

Plant, root, and soil microbiome

Changes of microbial population and N-cycling function genes with depth in three Chinese paddy soils – Huanhuan Wang, PLOS One

Water and extremophile microbiome

Candidatus Nitrosocaldus cavascurensis, an ammonia oxidizing, extremely thermophilic archaeon with a highly mobile genome – Sophie S Abby, bioRxiv

Microbes in the news

Artificial intelligence identifies bacteria images quickly, accurately – Greg Slabodkin, Health Data Management

Microbes on the market

Assembly Biosciences, Inc. (ASMB) Reaches $45.08 After 7.00% Up Move; GEOX SPA (GXSBF) Shorts Raised By 18.36% – Stephen Andrade, Herald KS

December 29, 2017

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It’s a bit quiet towards the end of the year, but not without highlights. Could we fight antibiotic resistance by targeting mild infections using alternative drugs? Do we want to correct our own genes using CRISPR and what’s the future for penicillin?

Jobs

Associate Professor – Microbiology – Dental College -chennai

General microbiology

Efficient Hydrogen-Dependent Carbon Dioxide Reduction by Escherichia coli – Magali Roger et al. – Current Biology

Press: Bacteria under pressure run reaction in reverse to sequester carbon – John Timmer – Ars Technica

The Role of Type VI Secretion System Effectors in Target Cell Lysis and Subsequent Horizontal Gene Transfer – Peter David Ringel et al. – Cell Reports

Press: Predatory Bacteria Acquire Drug Resistance Directly from Rivals – Genetic Engineering & Biotechnology News

* Alternative therapeutics for self-limiting infections—An indirect approach to the antibiotic resistance challenge – Kristofer Wollein Waldetoft and Sam P. Brown – PLoS Biology

Author interview: Alternatives to Antibiotics: Why managing mild maladies matters – Beth Baker – PLoS Research News

Animal experiments

Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets – María Carla Piazzon et al. – Microbiome

Animal microbiome

Mosquito vector-associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod-borne diseases – Panpim Thongsripong et al. – Ecology and Evolution

Plant, root and soil microbiome

Rhizosphere-associated Alcaligenes and Bacillus strains that induce resistance against blast and sheath blight diseases, enhance plant growth and improve mineral content in rice – Kaleem U. Kakar et al. – Journal of Applied Microbiology

Microbes in the news

A week of holiday junk food could derail your gut microbiome—but there’s hope – Claire Maldarelli – Popular Science

Microbiota and Cancer – Andrea S. Blevins Prime – Cancer Therapy Advisor

Maternal Antibiotic Exposure Affects Infant Fecal Microbiota Following Vaginal Delivery – Jessica Martin – Infectious Disease Advisor

Microbe expert claims we should wash them ‘AT LEAST’ once a week at a high temperature to avoid dust mites and bacteria – Unity Blott – Daily Mail

* CORRECTING THE GENES – Santanu Chakraborty – Bangalore Mirror

Govt study finds faecal bacteria in 97 percent ‘filtered’ water jars in Dhaka – Bdnews24

* 200 million lives saved – but prognosis for penicillin is not healthy – Harry Ridgewell and Angela Long (collaborator) – Wiki Tribune

Microbes on the market

Report on sale: Human Microbiome Therapeutics Market is expected to Witness a CAGR of 14.19 % Till 2022 including Key Players: Rebiotix, Seres Therapeutics – Craig Francis – Social Articles Tracking & PR news.com

Report on sale: Microbiome Drugs Market by Production, Capacity Utilization Rate, Ex-Factory Price, Revenue, Cost, Gross and Gross Margin Analysis – Amit Pawar – Social Articles Tracking & PR news.com

 

December 26, 2017

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Quite a few articles today especially in the plant/soil and water/extremophile sections. Plus: a new zebrafish model of the human gut microbiome, fiber and bifidos protect against north american diet-induced increased gut permeability in mice, prebiotics from the Morinda plant not only alter the gut microbiome but improve Alzheimers-like symptoms in a rat model, micro-eukaryotes may be an important factor in a deadly skin fungus infection in the Cascades Frog, and a new Leaf-FISH technique to visualize bacterial communities on plants. Happy Holidays!

Human oral microbiome

The oral microbiome—the relevant reservoir for acute pediatric appendicitis? – Carlotta Blod – International Journal of Colorectal Disease

Differences in carbon source usage by dental plaque in children with and without early childhood caries – Yan Zhao – International Journal of Oral Science

Review: Task Force on Design and Analysis in Oral Health Research: Host-Microbiome Interactions in Dysbiosis – T.E. Van Dyke – JDR Clinical & Translational Research

Human gut microbiome

Review: Probiotics and necrotizing enterocolitis – Ravi Mangal Patel – Seminars in Pediatric Surgery

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Animal experiments

Fusimonas intestini gen. nov., sp. nov., a novel intestinal bacterium of the family Lachnospiraceae associated with diabetes in mice – Hiroyuki Kusada – Scientific Reports

*Zebrafish Axenic Larvae Colonization with Human Intestinal Microbiota – Arias-Jayo Nerea – Zebrafish

*Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration – Bjoern O. Schroeder – Cell Host & Microbe

In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host – William A. Bryant – Frontiers in Microbiology

*Prebiotic Effect of Fructooligosaccharides from Morinda officinalis on Alzheimer’s Disease in Rodent Models by Targeting the Microbiota-Gut-Brain Axis – Diling Chen – Frontiers in Aging Neuroscience

Animal microbiome

Effect of Environmental Factors and an Emerging Parasitic Disease on Gut Microbiome of Wild Salmonid Fish – Anti Vasemägi – mSphere

*Composition of Micro-eukaryotes on the Skin of the Cascades Frog (Rana cascadae) and Patterns of Correlation between Skin Microbes and Batrachochytrium dendrobatidis – Jordan G. Kueneman – Frontiers in Microbiology

Plant, root, and soil microbiome

Chemical investigation of metabolites produced by an endophytic fungi Phialemonium curvatum from the leaves of Passiflora edulis –  G. R. Nalin Rathnayake – Natural Product Research

Novel hydrocarbonoclastic metal-tolerant Acinetobacter and Pseudomonas strains from Aconcagua river oil-polluted soil – Valentina Méndez – Journal of soil science and plant nutrition

Spatial patterns of enzyme activities in the rhizosphere: Effects of root hairs and root radius – Xiaomin Ma – Soil Biology and Biochemistry

The rhizosphere microbial community response to a bio-organic fertilizer: finding the mechanisms behind the suppression of watermelon Fusarium wilt disease – Jia Zhao – Acta Physiologiae Plantarum

Efficiency of two inoculation methods of Pseudomonas putida on growth and yield of tomato plants – Luis G. Hernández-Montiel – Journal of soil science and plant nutrition

Rhizospere yeasts improve P uptake of a maize arbuscular mycorrhizal association – Marcela Sarabia – Applied Soil Ecology

Ammonia-oxidizing microorganisms: key players in the promotion of plant growth – Adenike Eunice Amoo – Journal of soil science and plant nutrition

Review: Potassium solubilizing bacteria (KSB): Mechanisms, promotion of plant growth, and future prospects ­ A review – H. Etesami – Journal of soil science and plant nutrition

Long-term phosphorus fertilization effects on arbuscular mycorrhizal fungal diversity in Uruguayan grasses – Silvina García – Journal of soil science and plant nutrition

Alcaligenes faecalisassociated with Mimosa calodendron rizhosphere assist plant survival in arsenic rich soils – Érica Barbosa Felestrino – Journal of soil science and plant nutrition

Functional land-use change effects on soil fungal communities in Chilean temperate rainforests – César Marín – Journal of soil science and plant nutrition

Probiotic strain Stenotrophomonas acidaminiphila BJ1 degrades and reduces chlorothalonil toxicity to soil enzymes, microbial communities and plant roots – Qingming Zhang – AMB Express

Low light availability alters root exudation and reduces putative beneficial microorganisms in seagrass roots –  Belinda C. Martin – Frontiers in Microbiology

Effects of biochar on nutrients and the microbial community structure of tobacco-planting soils – Gao Lin – Journal of soil science and plant nutrition

Root-associated bacterial and fungal community profiles of Arabidopsis thaliana are robust across contrasting soil P levels – Chanz Robbins – Phytobiomes

Water and extremophile microbiome

Biogeographical patterns of bacterial and archaeal communities from distant hypersaline environments – M.R. Mora-Ruiz del – Systematic and Applied Microbiology

Cloning, Over-Expression, and Purification of Carbonic Anhydrase from an Extremophilic Bacterium: An Introduction to Advanced Molecular Biology – Vijayakumar Somalinga – The American Biology Teacher

Salinivibrio kushneri sp. nov., a moderately halophilic bacterium isolated from salterns – Clara López-Hermoso – Systematic and Applied Microbiology

Genome sequencing and heterologous expression of antiporters reveal alkaline response mechanisms of Halomonas alkalicola – Lei Zhai – Extremophiles

Benthic phototrophic community from Kiran soda lake, south-eastern Siberia – Ekaterina I. Burganskaya – Extremophiles

Enhancing the adaptability of the deep-sea bacterium Shewanella piezotolerans WP3 to high pressure and low temperature by experimental evolution under H2O2 stress – Zhe Xie – Applied and Environmental Microbiology

Fungal community structure at pelagic and littoral sites in Lake Biwa determined with high-throughput sequencing – Peixue Song – Limnology

Spatiotemporal dynamics of marine bacterial and archaeal communities in surface waters off the northern Antarctic Peninsula – Camila N. Signori – Deep Sea Research Part II: Topical Studies in Oceanography

Microbial Ecology

Dissertation: The Macroecology of Microorganisms: From Pattern to Process – David Clark – University of Essex

Review: Using metabolic networks to resolve ecological properties of microbiomes – Emilie E.L. Muller – Current Opinion in Systems Biology

Microbial stress mediated intercellular nanotubes in an anaerobic microbial consortium digesting cellulose – Martina John – Scientific Reports

Built environment

Distribution of Legionella and bacterial community composition among regionally diverse US cooling towers – Anna C. Llewellyn – PLOS one

Food microbiology

Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas – Kai-Yao Huang – BMC Systems Biology

Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks – Aaron M. Walsh – Applied and Environmental Microbiology

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Probiotics / prebiotics

Review: Recent Development of Prebiotic Research—Statement from an Expert Workshop – Giorgio La Fata – Nutrients

Effects of fermented soymilk with Lactobacillus casei Shirota on skin condition and the gut microbiota: a randomised clinical pilot trial – T. Nagino – Beneficial Microbes

Phages and viruses

Novel ssDNA viruses detected in the virome of bleached, habitat-forming kelp Ecklonia radiata –  Douglas Beattie – Frontiers in Marine Science

Bioinformatics

Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples – Jake Lin – BMC Genomics

Techniques

*Leaf-FISH: Microscale imaging of bacterial taxa on phyllosphere –  Elena L. Peredo – Frontiers in Microbiology

A new suite of plasmid vectors for fluorescence-based imaging of root colonizing pseudomonads –  Rosemarie Wilton – Frontiers in Plant Science

Synthetic microbial consortia enable rapid assembly of pure translation machinery – Fernando Villarreal – Nature Chemical Biology

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Microbes in the news

Essential science: Link between gut microbes and despair – Tim Sandle – Digital Science

Enjoy the holidays, but don’t forget your fiber – Tim Sandle – Digital Science

 

December 25, 2017

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A short digest today covering the human oral and gut microbiome, animal experiments, animal microbiome, plant, root and soil microbiome, techniques and news. At last we also have some “Lab stock fun picks”. Merry Christmas!!

 

Human oral microbiome

The oral microbiome-the relevant reservoir for acute pediatric appendicitis? – C Blod – International Journal of Colorectal Disease

 

 

Human gut microbiome

Intestinal microbiome analysis revealed dysbiosis in sickle cell disease – SH Lim – American Journal of Hematology

 

Animal experiments 

Fermented Soybean Meal Increases Lactic Acid Bacteria in Gut Microbiota of Atlantic Salmon (Salmo salar). – N Catalán – Probiotics and Antimicrobial Proteins

 

Animal microbiome 

The Combined Effect of Temperature and Host Clonal Line on the Microbiota of a Planktonic Crustacean. – KE Sullam – Microbial Ecology

 

Plant, root, and soil microbiome

Grey relational analysis for evaluating the effects of different rates of wine lees-derived biochar application on a plant-soil system with multi-metal contamination. – M Xu – Environmental Science and Pollution Research International

http://Transcriptomic responses of catalase, peroxidase and laccase encoding genes and enzymatic activities of oil spill inhabiting rhizospheric fungal strains. – MD Asemoloye – Environmental Pollution

Augmentation with potential endophytes enhances phytostabilization of Cr in contaminated soil. – MT Ahsan – Environmental Science and Pollution Research International

 

 

Techniques

Strain profiling and epidemiology of bacterial species from metagenomic sequencing – D Albanese – Nature Communications

Mechanistic and structural insight into promiscuity based metabolism of cardiac drug digoxin by gut microbial enzyme – K Kumar – Journal of Cellular Biochemistry

 

Microbes in the news

Cooking a turkey? Here’s how to make sure you avoid getting food poisoning – thejournal.ie

How the US military killed an Irishman in San Fran with germ warfare – Irish Central

How to avoid getting sick from flying – keep clean, stay hydrated and try to get a window seat – South China Morning Post

It’s getting real tough to ‘ESKAPE’ hospital-acquired infections – Indian Express

 

Lab stock funny picks (source: Shutterstock)

My magnifying glass is more powerful than the microscope

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Sometimes I try to incorporate the additive model of primary colours in my research: Red, Green , Blue!!

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Seems some one has finally been able to culture virus on a solid (agar) medium..

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Do you see what I see?

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